Read data

source(paste0(root.dir, 'scripts/myRLib.R'))
funcset <- readLines(paste0(root.dir, 'output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/sig_subset.set'))
funcset <- parseFuncSet(funcset)
funcset.names <- names(funcset)
xtyi.files <- strsplit('output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e+00.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-04.assoc.logistic:output-direction_XT_YI/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
ps <- strsplit('1,0.3,0.1,0.03,0.01,0.003,0.001,0.0003,0.0001', ',')[[1]]
inter.files <- strsplit('output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e+00.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-04.assoc.logistic:output-run_step2/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
prs.files <- strsplit('../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e+00.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-01.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-01.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-02.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-02.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-03.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-03.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-04.txt:../step1/output-run_step1/MAGNETIC_Serum.TG__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-04.txt', ':')[[1]]

Epistasis

for (i in 1:length(xtyi.files)) {
    cat("##", funcset.names[i])
    cat("
")
    cat("
")
    snp.subset <- funcset[[funcset.names[i]]]
    
    # read I ~ SNP
    prs <- read.table(paste0(root.dir, prs.files[i]), header = T)
    prs$sid <- as.character(prs$sid)
    prs.sub <- prs[prs$sid %in% snp.subset, ]
    
    # read others
    xtyi <- read.table(paste0(root.dir, xtyi.files[i]), header = T)
    xtyi$SNP <- as.character(xtyi$SNP)
    yt.xtyi <- xtyi[(xtyi$SNP %in% snp.subset) & (xtyi$SNP %in% 
        prs.sub$sid), ]
    yt.xtyi.xt <- yt.xtyi[yt.xtyi$TEST == "ADD", ]
    yt.xtyi.yi <- yt.xtyi[yt.xtyi$TEST == "PRS", ]
    inter <- read.table(paste0(root.dir, inter.files[i]), header = T)
    inter$SNP <- as.character(inter$SNP)
    inter <- inter[inter$TEST == "ADDxPRS", ]
    yt.inter <- inter[(inter$SNP %in% snp.subset) & (inter$SNP %in% 
        prs.sub$sid), ]
    
    # order all rows
    yt.xtyi.xt <- yt.xtyi.xt[order(yt.xtyi.xt$SNP), ]
    yt.xtyi.yi <- yt.xtyi.yi[order(yt.xtyi.yi$SNP), ]
    yt.inter <- yt.inter[order(yt.inter$SNP), ]
    prs.sub <- prs.sub[order(prs.sub$sid), ]
    
    # check direction
    prs.sub$nt1 <- as.character(prs.sub$nt1)
    yt.xtyi.xt$A1 <- as.character(yt.xtyi.xt$A1)
    yt.inter$A1 <- as.character(yt.inter$A1)
    if (sum(prs.sub$nt1 != yt.xtyi.xt$A1) != 0 | sum(prs.sub$nt1 != 
        yt.inter$A1) != 0) {
        print("Direction does not match. Exit!")
        quit()
    }
    
    yt.xtyi.xt.mean.std <- getMeanStd(yt.xtyi.xt$SNP, yt.xtyi.xt$P, 
        yt.xtyi.xt$OR, "Y~Gi+I (Gi)")
    yt.xtyi.yi.mean.std <- getMeanStd(yt.xtyi.yi$SNP, yt.xtyi.yi$P, 
        yt.xtyi.yi$OR, "Y~Gi+I (I)")
    yt.inter.mean.std <- getMeanStd(yt.inter$SNP, yt.inter$P, 
        yt.inter$OR, "Y~Gi*I")
    prs.sub.mean.std <- data.frame(SNP = prs.sub$sid, Mean = prs.sub$ldpred_beta, 
        Std = 0, Type = "I~Gi")
    
    # create data frame for plot
    df <- rbind(yt.xtyi.xt.mean.std, yt.xtyi.yi.mean.std, prs.sub.mean.std, 
        yt.inter.mean.std)
    ratio <- max(1, nrow(yt.inter)/40)
    cat
    p <- ggplot(df) + geom_point(aes(x = SNP, y = Mean)) + geom_errorbar(aes(x = SNP, 
        ymin = Mean - 1.96 * Std, ymax = Mean + 1.96 * Std), 
        colour = "black", width = 0.1) + geom_hline(yintercept = 0, 
        color = "red") + facet_grid(. ~ Type, scales = "free_x") + 
        coord_flip() + theme(axis.text.x = element_text(angle = 90, 
        hjust = 1))
    p2 <- ggplot(yt.inter) + geom_bar(aes(x = SNP, y = -log10(P)), 
        stat = "identity") + coord_flip() + ggtitle("Interaction P-value")
    subchunkify(p, ratio)
    subchunkify(p2, ratio)
    cat("
")
    inter.plus.gwas.pval <- cbind(yt.inter, yt.xtyi.xt$P)
    colnames(inter.plus.gwas.pval) <- c(colnames(yt.inter), "GWAS.P")
    pander(inter.plus.gwas.pval[order(inter.plus.gwas.pval$P, 
        decreasing = F), ])
    cat("
")
    cat("
")
}

p1.0000e+00

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 1.667 2.256 0.02408 2.361e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.504 1.873 0.061 3.405e-05
81 9 rs564398 0 C ADDxPRS 4864 1.28 1.86 0.06288 8.749e-09
84 9 rs7865618 0 G ADDxPRS 4864 1.266 1.783 0.07464 1.304e-09
120 14 rs10431700 0 G ADDxPRS 4864 0.8035 -1.664 0.09612 2.836e-05
60 9 rs523096 0 G ADDxPRS 4864 1.172 1.205 0.2281 1.374e-06
111 10 rs7910044 0 A ADDxPRS 4864 0.8578 -1.163 0.2447 2.958e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.8611 -1.141 0.2537 1.219e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.8661 -1.1 0.2712 5.112e-10
87 9 rs10965219 0 G ADDxPRS 4864 0.8719 -1.05 0.2939 7.001e-11
150 22 rs688034 0 T ADDxPRS 4864 0.8691 -1.031 0.3026 1.002e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.138 0.9836 0.3253 5.93e-14
102 9 rs1333042 0 A ADDxPRS 4864 1.119 0.8637 0.3877 1.592e-12
126 16 rs7199903 0 T ADDxPRS 4864 0.894 -0.8474 0.3968 1.945e-05
3 1 rs10914783 0 A ADDxPRS 4864 1.297 0.8037 0.4216 3.355e-06
54 8 rs16872634 0 C ADDxPRS 4864 0.8942 -0.789 0.4301 3.816e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9049 -0.7088 0.4785 3.598e-05
99 9 rs2891168 0 A ADDxPRS 4864 1.097 0.7067 0.4797 5.962e-13
141 20 rs6071469 0 C ADDxPRS 4864 0.9066 -0.6948 0.4872 3.574e-05
30 4 rs11939435 0 G ADDxPRS 4864 1.161 0.6833 0.4944 3.181e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.091 0.6686 0.5038 6.726e-13
132 17 rs6502872 0 T ADDxPRS 4864 0.921 -0.635 0.5254 4.189e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.108 0.6208 0.5347 9.71e-06
21 2 rs2943634 0 A ADDxPRS 4864 1.088 0.601 0.5478 1.418e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9226 -0.5529 0.5803 1.444e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.093 0.5475 0.5841 3.191e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9304 -0.4928 0.6222 1.284e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9393 -0.4714 0.6373 2.272e-07
147 21 rs2838756 0 C ADDxPRS 4864 1.053 0.3567 0.7213 2.613e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9466 -0.3268 0.7438 3.286e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.042 0.3119 0.7551 1.233e-13
48 6 rs6922269 0 A ADDxPRS 4864 1.044 0.2912 0.7709 6.912e-06
42 5 rs565928 0 T ADDxPRS 4864 0.9752 -0.1541 0.8775 6.18e-06
39 5 rs436495 0 A ADDxPRS 4864 0.9785 -0.1339 0.8935 7.912e-06
9 1 rs2883720 0 T ADDxPRS 4864 1.017 0.1272 0.8988 4.593e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9898 -0.06436 0.9487 2.717e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.006 0.04105 0.9673 4.041e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9981 -0.01143 0.9909 5.738e-06

p3.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 1.686 2.365 0.01804 2.366e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.52 1.975 0.04824 3.394e-05
81 9 rs564398 0 C ADDxPRS 4864 1.22 1.544 0.1226 9.12e-09
120 14 rs10431700 0 G ADDxPRS 4864 0.823 -1.533 0.1254 2.786e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.21 1.486 0.1372 1.357e-09
111 10 rs7910044 0 A ADDxPRS 4864 0.873 -1.063 0.2877 2.893e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.8775 -1.028 0.3039 1.237e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.8812 -0.9978 0.3184 5.229e-10
135 19 rs7250581 0 A ADDxPRS 4864 1.158 0.915 0.3602 9.688e-06
60 9 rs523096 0 G ADDxPRS 4864 1.122 0.9016 0.3673 1.432e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.8974 -0.8544 0.3929 7.155e-11
132 17 rs6502872 0 T ADDxPRS 4864 0.9008 -0.8339 0.4044 4.042e-05
150 22 rs688034 0 T ADDxPRS 4864 0.8976 -0.8199 0.4123 9.84e-06
144 20 rs2093154 0 T ADDxPRS 4864 0.8942 -0.8191 0.4127 3.51e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.8963 -0.8015 0.4228 3.49e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9025 -0.8015 0.4229 1.972e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.104 0.7793 0.4358 5.876e-14
3 1 rs10914783 0 A ADDxPRS 4864 1.245 0.713 0.4758 3.325e-06
21 2 rs2943634 0 A ADDxPRS 4864 1.099 0.6945 0.4874 1.449e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9072 -0.6902 0.4901 1.435e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.091 0.6843 0.4938 1.574e-12
54 8 rs16872634 0 C ADDxPRS 4864 0.9103 -0.6825 0.4949 3.889e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9132 -0.6413 0.5214 1.276e-05
30 4 rs11939435 0 G ADDxPRS 4864 1.137 0.6046 0.5454 3.157e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.071 0.4907 0.6237 2.589e-05
99 9 rs2891168 0 A ADDxPRS 4864 1.064 0.4879 0.6256 5.929e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.059 0.4499 0.6528 6.683e-13
123 16 rs12716963 0 G ADDxPRS 4864 1.064 0.3975 0.691 3.143e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9507 -0.3926 0.6946 2.317e-07
6 1 rs599839 0 G ADDxPRS 4864 0.9653 -0.2295 0.8185 2.787e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.969 -0.194 0.8462 3.283e-05
48 6 rs6922269 0 A ADDxPRS 4864 1.02 0.137 0.891 6.982e-06
138 20 rs6071467 0 G ADDxPRS 4864 0.9867 -0.09891 0.9212 3.972e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.012 0.09299 0.9259 1.228e-13
42 5 rs565928 0 T ADDxPRS 4864 0.9859 -0.09012 0.9282 6.025e-06
9 1 rs2883720 0 T ADDxPRS 4864 1.011 0.08724 0.9305 4.543e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9899 -0.06434 0.9487 7.72e-06
36 5 rs449650 0 T ADDxPRS 4864 1.005 0.03113 0.9752 5.601e-06

p1.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 1.567 2.43 0.01509 2.428e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.44 2.061 0.03933 3.435e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.221 1.51 0.131 1.003e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.8861 -1.172 0.2412 3.805e-05
120 14 rs10431700 0 G ADDxPRS 4864 0.8947 -1.068 0.2857 2.685e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.8886 -1.051 0.2934 3.268e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.8909 -1.027 0.3046 3.255e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9061 -0.8518 0.3943 1.374e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9079 -0.8329 0.4049 1.22e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.094 0.7909 0.429 2.535e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.089 0.7584 0.4482 1.435e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9278 -0.7156 0.4742 2.855e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.9279 -0.7125 0.4761 1.296e-09
81 9 rs564398 0 C ADDxPRS 4864 1.078 0.71 0.4777 1.045e-08
78 9 rs10965215 0 A ADDxPRS 4864 0.9286 -0.7069 0.4796 5.579e-10
84 9 rs7865618 0 G ADDxPRS 4864 1.076 0.6918 0.489 1.554e-09
126 16 rs7199903 0 T ADDxPRS 4864 0.9375 -0.6114 0.5409 2.026e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9366 -0.5175 0.6048 2.93e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9485 -0.4753 0.6346 3.79e-05
105 9 rs1333048 0 A ADDxPRS 4864 0.957 -0.4183 0.6757 1.233e-13
3 1 rs10914783 0 A ADDxPRS 4864 1.097 0.3806 0.7035 3.319e-06
30 4 rs11939435 0 G ADDxPRS 4864 1.064 0.3513 0.7254 3.139e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9643 -0.3477 0.728 7.682e-11
54 8 rs16872634 0 C ADDxPRS 4864 0.9626 -0.3327 0.7394 4.362e-05
150 22 rs688034 0 T ADDxPRS 4864 0.9689 -0.2916 0.7706 9.695e-06
93 9 rs6475606 0 C ADDxPRS 4864 1.027 0.2543 0.7992 5.895e-14
48 6 rs6922269 0 A ADDxPRS 4864 0.9727 -0.2386 0.8114 7.222e-06
66 9 rs10757264 0 G ADDxPRS 4864 0.9766 -0.2227 0.8238 2.422e-07
102 9 rs1333042 0 A ADDxPRS 4864 1.024 0.221 0.8251 1.56e-12
60 9 rs523096 0 G ADDxPRS 4864 1.017 0.1624 0.871 1.627e-06
18 2 rs17018897 0 G ADDxPRS 4864 1.013 0.09445 0.9248 3.186e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.9922 -0.07469 0.9405 6.684e-13
123 16 rs12716963 0 G ADDxPRS 4864 1.009 0.07082 0.9435 3.057e-05
36 5 rs449650 0 T ADDxPRS 4864 1.008 0.06155 0.9509 5.414e-06
99 9 rs2891168 0 A ADDxPRS 4864 0.9957 -0.04131 0.967 5.931e-13
39 5 rs436495 0 A ADDxPRS 4864 1.004 0.03239 0.9742 7.452e-06
9 1 rs2883720 0 T ADDxPRS 4864 0.9966 -0.03216 0.9743 4.341e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9999 -0.001157 0.9991 5.796e-06

p3.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
117 12 rs2167512 0 A ADDxPRS 4864 1.281 2.112 0.03465 2.534e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.173 1.943 0.05199 1.079e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.229 1.846 0.06492 3.527e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9083 -1.366 0.1718 3.022e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9098 -1.341 0.1799 3.011e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.923 -1.233 0.2177 3.754e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.074 1.004 0.3155 2.511e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9358 -0.9513 0.3414 3.618e-05
105 9 rs1333048 0 A ADDxPRS 4864 0.9493 -0.7818 0.4343 1.246e-13
15 1 rs17465637 0 T ADDxPRS 4864 0.947 -0.7524 0.4518 1.119e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9489 -0.7249 0.4685 1.264e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.046 0.6425 0.5206 1.336e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9568 -0.5526 0.5805 2.971e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.9687 -0.4759 0.6341 6.723e-13
48 6 rs6922269 0 A ADDxPRS 4864 0.9664 -0.475 0.6348 7.445e-06
99 9 rs2891168 0 A ADDxPRS 4864 0.9702 -0.4533 0.6503 5.95e-13
60 9 rs523096 0 G ADDxPRS 4864 0.9705 -0.4492 0.6533 1.823e-06
78 9 rs10965215 0 A ADDxPRS 4864 0.9725 -0.4237 0.6718 5.802e-10
126 16 rs7199903 0 T ADDxPRS 4864 0.9735 -0.4041 0.6861 2.025e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.9739 -0.4027 0.6872 1.337e-09
150 22 rs688034 0 T ADDxPRS 4864 1.019 0.277 0.7818 1.005e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.023 0.2683 0.7885 3.003e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.9824 -0.2631 0.7924 4.052e-05
120 14 rs10431700 0 G ADDxPRS 4864 0.9845 -0.2408 0.8097 2.596e-05
102 9 rs1333042 0 A ADDxPRS 4864 0.9864 -0.2043 0.8381 1.566e-12
93 9 rs6475606 0 C ADDxPRS 4864 0.9865 -0.2023 0.8397 6.038e-14
123 16 rs12716963 0 G ADDxPRS 4864 0.9842 -0.1995 0.8419 3.077e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.014 0.1978 0.8432 5.241e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9765 -0.1622 0.8712 3.347e-06
87 9 rs10965219 0 G ADDxPRS 4864 1.009 0.1429 0.8863 8.164e-11
111 10 rs7910044 0 A ADDxPRS 4864 0.9936 -0.09838 0.9216 2.977e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9938 -0.09343 0.9256 2.475e-07
30 4 rs11939435 0 G ADDxPRS 4864 0.9898 -0.09325 0.9257 3.159e-05
81 9 rs564398 0 C ADDxPRS 4864 0.9939 -0.09124 0.9273 1.178e-08
84 9 rs7865618 0 G ADDxPRS 4864 0.9947 -0.07885 0.9372 1.754e-09
39 5 rs436495 0 A ADDxPRS 4864 1.006 0.07236 0.9423 7.59e-06
42 5 rs565928 0 T ADDxPRS 4864 1.003 0.03857 0.9692 5.878e-06
36 5 rs449650 0 T ADDxPRS 4864 1.002 0.02817 0.9775 5.517e-06

p1.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.127 1.988 0.0468 1.123e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.16 1.728 0.08396 2.609e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.134 1.54 0.1237 3.61e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.927 -1.463 0.1434 2.954e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.928 -1.443 0.1492 2.94e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.939 -1.226 0.2202 3.588e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.057 1.064 0.2872 2.545e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9541 -0.9823 0.3259 3.864e-05
105 9 rs1333048 0 A ADDxPRS 4864 0.9549 -0.9378 0.3483 1.259e-13
96 9 rs4977574 0 A ADDxPRS 4864 0.9672 -0.6769 0.4985 6.813e-13
99 9 rs2891168 0 A ADDxPRS 4864 0.9679 -0.6624 0.5077 6.016e-13
60 9 rs523096 0 G ADDxPRS 4864 0.9685 -0.652 0.5144 1.869e-06
48 6 rs6922269 0 A ADDxPRS 4864 0.9683 -0.6114 0.5409 7.544e-06
15 1 rs17465637 0 T ADDxPRS 4864 0.9697 -0.5783 0.563 1.069e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9452 -0.5205 0.6027 3.399e-06
150 22 rs688034 0 T ADDxPRS 4864 1.026 0.5178 0.6046 1.049e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9729 -0.5172 0.605 1.213e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9717 -0.4868 0.6264 2.908e-05
102 9 rs1333042 0 A ADDxPRS 4864 0.9778 -0.4551 0.6491 1.594e-12
93 9 rs6475606 0 C ADDxPRS 4864 0.9779 -0.4532 0.6504 6.191e-14
84 9 rs7865618 0 G ADDxPRS 4864 0.9786 -0.4381 0.6613 1.814e-09
81 9 rs564398 0 C ADDxPRS 4864 0.979 -0.4289 0.668 1.217e-08
21 2 rs2943634 0 A ADDxPRS 4864 1.022 0.4175 0.6763 1.272e-05
87 9 rs10965219 0 G ADDxPRS 4864 1.019 0.3977 0.6908 8.257e-11
54 8 rs16872634 0 C ADDxPRS 4864 1.021 0.388 0.698 5.707e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.022 0.3529 0.7242 2.92e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9861 -0.287 0.7741 1.98e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.013 0.2773 0.7815 2.607e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9787 -0.2674 0.7891 3.171e-05
39 5 rs436495 0 A ADDxPRS 4864 1.016 0.2633 0.7923 7.819e-06
9 1 rs2883720 0 T ADDxPRS 4864 0.9872 -0.258 0.7964 3.899e-05
123 16 rs12716963 0 G ADDxPRS 4864 0.9851 -0.2535 0.7999 3.12e-05
42 5 rs565928 0 T ADDxPRS 4864 1.014 0.2369 0.8127 6.042e-06
78 9 rs10965215 0 A ADDxPRS 4864 0.9889 -0.2322 0.8164 5.793e-10
111 10 rs7910044 0 A ADDxPRS 4864 1.011 0.2315 0.8169 3.139e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.99 -0.2079 0.8353 1.339e-09
36 5 rs449650 0 T ADDxPRS 4864 1.011 0.1829 0.8549 5.681e-06
66 9 rs10757264 0 G ADDxPRS 4864 1.001 0.02685 0.9786 2.454e-07

p3.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.106 1.819 0.06889 1.141e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.128 1.542 0.123 2.663e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.109 1.384 0.1665 3.709e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9428 -1.243 0.2141 3.714e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9447 -1.194 0.2326 3.076e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9453 -1.179 0.2384 3.057e-05
105 9 rs1333048 0 A ADDxPRS 4864 0.9557 -0.9976 0.3185 1.272e-13
147 21 rs2838756 0 C ADDxPRS 4864 1.049 0.9963 0.3191 2.532e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9578 -0.8882 0.3744 7.545e-06
150 22 rs688034 0 T ADDxPRS 4864 1.039 0.8385 0.4018 1.099e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9639 -0.8353 0.4035 4.074e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.964 -0.8073 0.4195 6.957e-13
99 9 rs2891168 0 A ADDxPRS 4864 0.9643 -0.8001 0.4237 6.132e-13
3 1 rs10914783 0 A ADDxPRS 4864 0.9345 -0.6745 0.5 3.525e-06
15 1 rs17465637 0 T ADDxPRS 4864 0.9678 -0.6687 0.5037 1.063e-05
60 9 rs523096 0 G ADDxPRS 4864 0.9722 -0.6241 0.5326 1.847e-06
6 1 rs599839 0 G ADDxPRS 4864 0.9669 -0.619 0.5359 2.784e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9707 -0.6092 0.5424 1.21e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.025 0.5645 0.5724 2.694e-05
93 9 rs6475606 0 C ADDxPRS 4864 0.9747 -0.5642 0.5726 6.383e-14
18 2 rs17018897 0 G ADDxPRS 4864 1.033 0.5617 0.5743 2.895e-05
102 9 rs1333042 0 A ADDxPRS 4864 0.976 -0.5329 0.5941 1.641e-12
84 9 rs7865618 0 G ADDxPRS 4864 0.9768 -0.5168 0.6053 1.835e-09
81 9 rs564398 0 C ADDxPRS 4864 0.9783 -0.4829 0.6292 1.225e-08
54 8 rs16872634 0 C ADDxPRS 4864 1.023 0.4662 0.6411 5.771e-05
87 9 rs10965219 0 G ADDxPRS 4864 1.019 0.4214 0.6734 8.301e-11
39 5 rs436495 0 A ADDxPRS 4864 1.016 0.2893 0.7724 7.97e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.9793 -0.2858 0.775 3.209e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.013 0.2803 0.7793 1.227e-05
42 5 rs565928 0 T ADDxPRS 4864 1.014 0.2629 0.7926 6.157e-06
78 9 rs10965215 0 A ADDxPRS 4864 0.9912 -0.1995 0.8419 5.841e-10
75 9 rs7049105 0 G ADDxPRS 4864 0.9916 -0.1911 0.8485 1.349e-09
9 1 rs2883720 0 T ADDxPRS 4864 0.9916 -0.1827 0.855 3.89e-05
36 5 rs449650 0 T ADDxPRS 4864 1.009 0.1729 0.8627 5.791e-06
123 16 rs12716963 0 G ADDxPRS 4864 0.9914 -0.1568 0.8754 3.104e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.993 -0.1562 0.8759 1.936e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.005 0.1241 0.9013 3.364e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9997 -0.007641 0.9939 2.393e-07

p1.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.107 1.8 0.07183 1.154e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.122 1.431 0.1526 2.698e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.104 1.282 0.1998 3.778e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9452 -1.132 0.2576 7.502e-06
105 9 rs1333048 0 A ADDxPRS 4864 0.9491 -1.12 0.2628 1.3e-13
138 20 rs6071467 0 G ADDxPRS 4864 0.9471 -1.114 0.2652 3.801e-05
150 22 rs688034 0 T ADDxPRS 4864 1.052 1.064 0.2874 1.098e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.05 0.9927 0.3208 2.51e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.9556 -0.9759 0.3291 7.172e-13
99 9 rs2891168 0 A ADDxPRS 4864 0.9557 -0.9723 0.3309 6.318e-13
132 17 rs6502872 0 T ADDxPRS 4864 0.9589 -0.9264 0.3542 4.19e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9599 -0.8153 0.4149 1.074e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.049 0.8105 0.4176 2.888e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9617 -0.7977 0.425 3.171e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9623 -0.7842 0.4329 3.15e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9618 -0.7753 0.4381 1.225e-05
6 1 rs599839 0 G ADDxPRS 4864 0.958 -0.7721 0.4401 2.782e-05
93 9 rs6475606 0 C ADDxPRS 4864 0.9665 -0.7341 0.4629 6.594e-14
84 9 rs7865618 0 G ADDxPRS 4864 0.9685 -0.6869 0.4921 1.889e-09
60 9 rs523096 0 G ADDxPRS 4864 0.9696 -0.6657 0.5056 1.873e-06
3 1 rs10914783 0 A ADDxPRS 4864 0.9353 -0.6476 0.5172 3.661e-06
81 9 rs564398 0 C ADDxPRS 4864 0.9711 -0.6282 0.5299 1.261e-08
102 9 rs1333042 0 A ADDxPRS 4864 0.972 -0.6078 0.5433 1.698e-12
120 14 rs10431700 0 G ADDxPRS 4864 1.024 0.5292 0.5967 2.746e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.025 0.479 0.6319 5.794e-05
87 9 rs10965219 0 G ADDxPRS 4864 1.022 0.4778 0.6328 8.479e-11
21 2 rs2943634 0 A ADDxPRS 4864 1.011 0.2375 0.8123 1.244e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9898 -0.1379 0.8903 3.217e-05
39 5 rs436495 0 A ADDxPRS 4864 1.008 0.1361 0.8918 7.949e-06
123 16 rs12716963 0 G ADDxPRS 4864 0.9926 -0.1318 0.8952 3.074e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.9945 -0.1154 0.9081 3.971e-05
42 5 rs565928 0 T ADDxPRS 4864 1.006 0.1075 0.9144 6.134e-06
111 10 rs7910044 0 A ADDxPRS 4864 0.9955 -0.1024 0.9184 3.485e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.9957 -0.09423 0.9249 6.001e-10
75 9 rs7049105 0 G ADDxPRS 4864 0.9959 -0.09146 0.9271 1.38e-09
126 16 rs7199903 0 T ADDxPRS 4864 0.9976 -0.05275 0.9579 1.922e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9981 -0.04071 0.9675 2.397e-07
36 5 rs449650 0 T ADDxPRS 4864 1.001 0.01358 0.9892 5.778e-06

p3.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.107 1.702 0.08881 1.163e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.137 1.503 0.1329 2.678e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.118 1.357 0.1748 3.786e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9308 -1.356 0.1751 7.446e-06
105 9 rs1333048 0 A ADDxPRS 4864 0.9383 -1.282 0.1998 1.306e-13
150 22 rs688034 0 T ADDxPRS 4864 1.061 1.188 0.2347 1.086e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.9432 -1.182 0.237 7.28e-13
99 9 rs2891168 0 A ADDxPRS 4864 0.9435 -1.177 0.239 6.414e-13
132 17 rs6502872 0 T ADDxPRS 4864 0.9502 -1.059 0.2897 4.393e-05
6 1 rs599839 0 G ADDxPRS 4864 0.9445 -0.9667 0.3337 2.757e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.06 0.9358 0.3494 2.876e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9511 -0.9337 0.3505 1.096e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9528 -0.9296 0.3526 3.941e-05
93 9 rs6475606 0 C ADDxPRS 4864 0.9554 -0.9238 0.3556 6.737e-14
12 1 rs2133189 0 C ADDxPRS 4864 0.9519 -0.9193 0.3579 1.249e-05
84 9 rs7865618 0 G ADDxPRS 4864 0.9555 -0.9168 0.3592 1.883e-09
60 9 rs523096 0 G ADDxPRS 4864 0.958 -0.8698 0.3844 1.854e-06
81 9 rs564398 0 C ADDxPRS 4864 0.958 -0.8637 0.3878 1.255e-08
147 21 rs2838756 0 C ADDxPRS 4864 1.043 0.8034 0.4218 2.508e-05
102 9 rs1333042 0 A ADDxPRS 4864 0.9641 -0.7379 0.4606 1.731e-12
87 9 rs10965219 0 G ADDxPRS 4864 1.029 0.5895 0.5556 8.577e-11
3 1 rs10914783 0 A ADDxPRS 4864 0.9478 -0.4873 0.6261 3.751e-06
144 20 rs2093154 0 T ADDxPRS 4864 0.9779 -0.4267 0.6696 3.331e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9787 -0.4119 0.6804 3.309e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.02 0.4094 0.6823 2.836e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.021 0.3805 0.7036 5.615e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9838 -0.3462 0.7292 3.575e-05
123 16 rs12716963 0 G ADDxPRS 4864 0.9843 -0.2619 0.7934 3.106e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.013 0.2488 0.8035 1.246e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9824 -0.225 0.822 3.273e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.9943 -0.1128 0.9102 4.15e-05
126 16 rs7199903 0 T ADDxPRS 4864 1.005 0.1056 0.9159 1.938e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9945 -0.09208 0.9266 5.879e-06
75 9 rs7049105 0 G ADDxPRS 4864 1.004 0.08661 0.931 1.399e-09
78 9 rs10965215 0 A ADDxPRS 4864 1.004 0.08527 0.932 6.085e-10
39 5 rs436495 0 A ADDxPRS 4864 1.002 0.02874 0.9771 8.078e-06
66 9 rs10757264 0 G ADDxPRS 4864 1.001 0.01095 0.9913 2.389e-07
42 5 rs565928 0 T ADDxPRS 4864 0.9999 -0.002336 0.9981 6.241e-06

p1.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.115 1.704 0.08831 1.169e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9217 -1.445 0.1485 7.408e-06
105 9 rs1333048 0 A ADDxPRS 4864 0.9267 -1.438 0.1505 1.3e-13
117 12 rs2167512 0 A ADDxPRS 4864 1.137 1.407 0.1593 2.637e-05
96 9 rs4977574 0 A ADDxPRS 4864 0.9307 -1.364 0.1727 7.275e-13
99 9 rs2891168 0 A ADDxPRS 4864 0.9311 -1.357 0.1749 6.41e-13
114 12 rs2398486 0 T ADDxPRS 4864 1.114 1.236 0.2165 3.749e-05
84 9 rs7865618 0 G ADDxPRS 4864 0.9381 -1.206 0.2279 1.81e-09
150 22 rs688034 0 T ADDxPRS 4864 1.066 1.197 0.2315 1.079e-05
60 9 rs523096 0 G ADDxPRS 4864 0.9411 -1.152 0.2494 1.795e-06
6 1 rs599839 0 G ADDxPRS 4864 0.9303 -1.147 0.2512 2.719e-05
81 9 rs564398 0 C ADDxPRS 4864 0.9412 -1.142 0.2535 1.208e-08
93 9 rs6475606 0 C ADDxPRS 4864 0.9429 -1.118 0.2634 6.762e-14
132 17 rs6502872 0 T ADDxPRS 4864 0.9499 -0.9982 0.3182 4.541e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.066 0.9677 0.3332 2.912e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9473 -0.9463 0.344 1.116e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9484 -0.9266 0.3542 1.272e-05
102 9 rs1333042 0 A ADDxPRS 4864 0.9539 -0.8929 0.3719 1.74e-12
138 20 rs6071467 0 G ADDxPRS 4864 0.9546 -0.8348 0.4039 4.021e-05
87 9 rs10965219 0 G ADDxPRS 4864 1.039 0.7506 0.4529 8.435e-11
147 21 rs2838756 0 C ADDxPRS 4864 1.039 0.6772 0.4983 2.548e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9803 -0.3934 0.694 3.593e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.02 0.3916 0.6953 2.903e-05
123 16 rs12716963 0 G ADDxPRS 4864 0.9762 -0.3742 0.7083 3.177e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9594 -0.3524 0.7246 3.792e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.9731 -0.3257 0.7447 3.282e-05
78 9 rs10965215 0 A ADDxPRS 4864 1.016 0.3169 0.7513 5.975e-10
75 9 rs7049105 0 G ADDxPRS 4864 1.016 0.3117 0.7552 1.383e-09
21 2 rs2943634 0 A ADDxPRS 4864 1.015 0.269 0.788 1.243e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.015 0.2594 0.7953 5.433e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9858 -0.2557 0.7982 3.431e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9866 -0.2409 0.8097 3.407e-05
66 9 rs10757264 0 G ADDxPRS 4864 1.01 0.1866 0.8519 2.373e-07
126 16 rs7199903 0 T ADDxPRS 4864 1.008 0.1599 0.873 1.945e-05
39 5 rs436495 0 A ADDxPRS 4864 1.009 0.1396 0.889 8.18e-06
42 5 rs565928 0 T ADDxPRS 4864 1.007 0.1067 0.9151 6.332e-06
9 1 rs2883720 0 T ADDxPRS 4864 0.9985 -0.02742 0.9781 4.256e-05
36 5 rs449650 0 T ADDxPRS 4864 1.001 0.02031 0.9838 5.972e-06